From: Prioritising positively selected variants in whole-genome sequencing data using FineMAV
Information needed from the VCF file | Description | Mandatory VCF column |
---|---|---|
CHROM:POS | Chromosome number:position | Yes |
ID | Identifier | Yes |
REF | Reference base | Yes |
ALT | Alternative base | Yes |
AA | Ancestral allele | No |
CADD_PHRED | Phred-scaled Combined Annotation Dependent Depletion (CADD) score | No |
AF | Allele frequency (AF) for the alternative base. The AF should be reported for each population | No |